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NEXT_TASKS: log pending enrichment of single-edge DIET/syntrophy records #253

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realmarcin merged 1 commit into from
Jul 22, 2026
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NEXT_TASKS: log pending enrichment of single-edge DIET/syntrophy records #253

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14 changes: 14 additions & 0 deletions NEXT_TASKS.md
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Expand Up @@ -360,6 +360,20 @@ errors, e.g. sulfite → CHEBI:16731 *(E)-cinnamaldehyde* instead of CHEBI:17359
the primary full text isn't retrievable, keep edges to abstract-supported/directly-implied
claims and file the rest as a KNOWLEDGE_GAP (000176 is the worked example).

**PENDING — enrich the single-edge records via a full causal-graph run.** Six 2-node
records already carry one hand-authored `downstream` edge (donor→acceptor) from original
curation but have not had an Edison causal-graph pass: the DIET trio
`Geobacter_Clostridium_DIET` (000031, PMID:28287150),
`Geobacter_Methanosaeta_DIET` (000032, doi:10.1039/C3EE42189A),
`Geobacter_Methanosarcina_DIET` (000033, PMID:24837373); and the syntrophies
`Syntrophobacter_Methanobacterium_Syntrophy` (000068), `Syntrophobacter_Methanospirillum_Syntrophy`
(000069), `Syntrophomonas_Methanospirillum_Syntrophy` (000070). A full run could add
mechanistic nodes/edges (e.g. conductive pili / OmcS-OmcZ cytochromes, conductive-material
mediation, formate-vs-H2 routes, reverse/feedback edges) beyond the single existing edge.
Run `just research-community-causal CommunityMech:0000NN` per record, then curate
conservatively as usual. NB: stray untracked `*.yaml.bak` backups exist alongside these in
`kb/communities/` (gitignored, not in the repo) — target the `.yaml` files.

**Edison auth (resolved 2026-07-21):** the key was refreshed in `.env`
(`EDISON_API_KEY`) and authenticates (HTTP 200). The stale-key shadowing footgun is
**fixed in the runner** (#245): `load_api_key()` now treats the repo `.env` FILE as the
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